Quantitative UV lesion footprinting by Capture CPD-seq

Several decades ago, it was shown that proteins binding to DNA can quantitatively alter formation of DNA damage induced by UV light. This established the principle of UV footprinting to study protein-DNA contacts, non-intrusively in living cells, albeit at the limited precision and scale dictated by gel-based assays. Here, we expose cells or naked DNA to UV light followed by deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing (Capture CPD-seq). Combined across replicates, we mapped on average 166 CPDs per individual dipyrimidine position in the assayed regions, allowing per-base quantification of local stimulatory as well as inhibitory effects. Several transcription factors exhibited distinct and repeatable CPD damage signatures indicative of site occupancy, involving strong (up to 17-fold) position-specific elevations and inhibitions relative to unbound DNA. Positive damage modulation at some ETS transcription factor binding sites coincided at base-level with melanoma somatic mutation hotspots. Our work reveals widespread and potent modulation of UV damage by proteins in regulatory regions, largely obscured in sparse genome-wide CPD data as the net damage burden stays constant, while providing proof of principle for base-resolution study of protein-DNA interactions using light and sequencing.